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1

Synthesis and Characterization of Triflate Intermediate

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Example 4

FAB (HRMS) spectra were recorded with a LCT Premier (Waters Corp., Milford, Mass.).

The purity of all compounds was determined to be >95% as determined by 1H NMR and 13C NMR spectra, unless otherwise noted. The most active 5 compounds were verified for >95% purity by HPLC analyses. TLC was performed on glass backed silica gel plates (Uniplate) with spots visualized by UV light. All solvents were reagent grade and, when necessary, were purified and dried by standard methods. Concentration of solutions after reactions and extractions involved the use of a rotary evaporator operating at reduced pressure.

Example 5. Synthesis of 5-(benzyloxy)-2-formylphenyl trifluoromethanesulfonate (3): A solution of phenol 2 (11.2 g, mmol) in anhydrous DCM (245 mL) was stirred at 0° C. and triethylamine (10.2 mL, 73.5 mmol) was added followed by triflic anhydride (13.8 mL, 63.5 mmol) over 5 minutes. Upon completion the reaction was quenched by addition of water (50 mL), washed with saturated aqueous NaCl solution, dried (Na2SO4), filtered and concentrated. The residue was purified by column chromatography (SiO2, 4:1, Hex:EtOAc) to afford triflate 3 as a yellow oil (8.4 g, 23.6 mmol, 48%). Immediately used in Suzuki coupling reactions.

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2

Characterization of Chemical Compounds

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1H NMR were recorded at 400 or 500 MHz (Bruker DRX-400 Bruker with a H/C/P/F QNP gradient probe) spectrometer and 13C NMR spectra were recorded at 125 MHz (Bruker DRX 500 with broadband, inverse triple resonance, and high resolution magic angle spinning, HR-MA probe spectrometer); chemical shifts are reported in δ (ppm) relative to the internal chloroform-d (CDCl3, 7.27 ppm). FAB (HRMS) spectra were recorded with a LCT Premier (Waters Corp., Milford, MA). The purity of all compounds was determined to be >95% purity as determined by 1H NMR and 13C NMR spectra, unless otherwise noted. The most active five compounds were verified for >95% purity by HPLC analyses. TLC was performed on glass backed silica gel plates (Uniplate) with spots visualized by UV light. All solvents were reagent grade and, when necessary, were purified and dried by standard methods. Concentration of solutions after reactions and extractions involved the use of a rotary evaporator operating at reduced pressure.
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3

Metabolite Fingerprinting Analysis via UPLC

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For metabolite fingerprinting analysis an ultraperformance liquid chromatography system coupled to the photo diode array detector eλ (Waters Corp., Milford, MA, USA) and the high‐resolution orthogonal time‐of‐flight MS (HR‐MS) LCT Premier (Waters) was used as previously described (Feussner & Feussner, 2019). Samples of the polar and the nonpolar extraction phases were analysed in the positive and in the negative electrospray ionization (ESI) mode, resulting in four datasets.
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4

Ion Mobility Mass Spectrometry of Protein Complexes

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Mass spectra of protein samples (12–150 μM in 200 mM ammonium acetate, pH 7.8) were acquired in the positive-ion mode using a Synapt HDMS (Waters, UK), with quadrupole-orthogonal acceleration time-of­-flight geometry and a built-in traveling wave ion mobility device. Protein mass spectra were also acquired using the LCT Premier (Waters, UK) specially modified for the analysis of non-­covalently bound macromolecular complexes. The ESI conditions were optimized for the highest sensitivity detection of multimeric complexes in the gas phase (30 (link)). The drift times for the IMS data have been extracted using MassLynx software and the m/z spectra were plotted against the drift time using Driftscope software (Waters, UK). Calibration of the drift time cross-section was done by the combined analyses of denatured proteins (equine cytochrome c, β-lactoglobulin, avidin, alcohol dehydrogenase, pyruvate kinase). For each protein, the individual charge state ions were identified by m/z ratios and their measured drift times were plotted against collision cross-sections (Ω), taken from Prof. D. Clemmer's database (Indiana University Bloomington), as described previously (31 ,32 (link)).
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5

Spectroscopic Characterization Techniques

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NMR spectra were
obtained on Bruker
AV 500 and DRX 500 MHz spectrometers. 1H NMR spectra were
acquired with a relaxation delay of 2 s for small molecules and 30
s for polymers. UV–vis spectroscopy was performed using a Biomate
5 Thermo Spectronic spectrometer or Thermo Scientific NanoDrop 2000
(for small quantities). ESI-MS data were gathered on a Waters LCT
premier with ACQUITY LC. Infrared absorption spectra were recorded
using a PerkinElmer FT-IR equipped with an ATR accessory. Photoreactions
were carried out in a photochemical safety cabinet equipped with a
broadband, medium pressure Ace-Hanocia 7825–34 quartz mercury
arc lamp and ACE Glass Inc. power supply. Matrix-assisted laser desorption/ionization
time-of-flight mass (MALDI-TOF MS) spectrometry data was gathered
using sinapic acid (SA) as a matrix on an Applied Biosystems Voyager-DE-STR
spectrometer.
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6

Inert Atmosphere Synthesis and Characterization

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All reactions were carried out within a Schlenk line system under an inert atmosphere of argon. Commercially available reagents were utilized as received, without additional purification. In contrast, solvents underwent distillation following standard procedures prior to use. Column chromatography was generally performed on a silica gel (200–300 mesh), and elution was performed with petroleum ether and ethyl acetate. 1H and 13C NMR spectra were recorded on a Bruker DP-X500 MHz spectrometer (Bruker Corporation, Beijing, China). Chemical shifts were reported in ppm relative to internal tetramethylsilane for 1H NMR and CDCl3 (77.16 ppm) for 13C NMR. High-resolution mass spectra (HRMS) were collected on Waters LCT Premier™ with an ESI mass spectrometer (Waters Corporation, Beijing, China). Optical rotations were determined by a Rudolph Research Analytical AUTOPOL-IV. Melting points were measured on a STUART-SMP3 Melt-Temp apparatus without correction (Stuart Equipment, Beijing, China).
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7

Purification and Characterization of PNA Oligomers

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Purification was performed on an Agilent (Santa Clara, CA) 1200 Series RP-HPLC with automatic fraction collection using UV detection at 260 nm. Waters (Milford, MA) XBridge C18 (10 × 250 mm, 5 μm) columns were used in conjunction with Solvents A and B. Solvent A was 0.05% TFA in water and Solvent B consisted of 90% ACN in water. PNA HPLC isolates were characterized using ESI-MS on a Waters/Micromass LCT Premier time-of-flight mass spectrometer. The instrument was operated in W-mode at a nominal resolution of 10,000. The electrospray capillary voltage was 2 kV and the sample cone voltage was 60 V. The desolvation temperature was 275 °C and the desolvation gas was N2 with a flow of 300 L/h. Accurate masses were obtained using the internal reference standard method. The sample was introduced into the mass spectrometer via the direct loop injection method. Deconvolution of multiply charged ions was performed with MaxEnt I. All PNA oligomers gave molecular ions consistent with the calculated theoretical product values (Supplementary Table 1).
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8

Characterization of Organic Compounds by NMR and Mass Spectrometry

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1H NMR were recorded at 400 or 500 MHz (Bruker DRX- 400 Bruker with a H/C/P/F QNP gradient probe) spectrometer and 13C NMR spectra were recorded at 125 MHz (Bruker DRX 500 with broadband, inverse triple resonance, and high resolution magic angle spinning HR-MA probe spectrometer); chemical shifts are reported in δ (ppm) relative to the internal reference CDCl3-d (CDCl3, 7.27 ppm). FAB (HRMS) spectra were recorded with a LCT Premier (Waters Corp., Milford, MA) spectrometer. The purity of all compounds was determined to be >95% as determined by 1H NMR and 13C NMR spectra, unless otherwise noted. TLC was performed on glass- backed silica gel plates (Uniplate) with spots visualized by UV light. All solvents were reagent grade and, when necessary, were purified and dried by standard methods. Concentration of solutions after reactions and extractions involved the use of a rotary evaporator operating at reduced pressure.
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9

Microwave-assisted Synthesis of Novel Compounds

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All reagents and solvents were used as purchased from commercial suppliers or were purified/dried according to Armarego and Chai [28 ]. Purifications by column chromatography on silica gel were performed using Merck Silica Gel 60 (70–230 mesh). 1H and 13C NMR spectra were recorded on Bruker ARX500 instruments using CDCl3 as an internal reference. Chemical shifts (δ values) are given in parts per million (ppm), and the multiplicity of signals is reported as follows: s, singlet; bs, broad singlet; d, doublet; t, triplet; q, quartet; dd, doublet of doublets; m, multiplet. HRMS analyses were performed using a Waters LCT Premier instrument by positive ion mode ElectroSpray Ionization (ESI+). A Monowave 50 appartus from Anton-Paar was used with a thermic control (Pmax: 315 W).
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10

Mass Spectrometric Analysis of FAD-Compound Adducts

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Human recombinant LSD1 protein (125 μM) was treated with 1 mM TAK-418 at room temperature for 1 hour in 50 mM tris-HCl (pH 8.0) to form TAK-418 adducts on FAD in LSD1. Subsequently, the protein samples were denatured on ice with adding 8 M urea solution to a final concentration of 6.4 M for 1 hour, and the FAD-compound adducts were extracted on ice with acetonitrile for 15 min. The precipitates were removed by centrifugation. The supernatants were added 500 mM ammonium acetate to a final concentration of 5 mM and were subjected to electrospray ionization (ESI) mass spectrometric analysis. The samples containing FAD-compound adducts were analyzed by Waters LCT premier, single time-of-flight (TOF) liquid chromatography–mass spectrometry (LC-MS) system, using the negative ion detection mode. Unizon UK-18 (Imtakt) was used for LC separation column, and 10 mM ammonium acetate was used for LC solvent. The eluate was carried out with 0 to 100% acetonitrile. Column and solvent were chilled with ice for suppressing degradation of the FAD-compound adducts during all the procedure.
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